+ const franklin = `
F
`;
- const color = data.preferred ? "w3-text-flat-peter-river" : "";
- const starIcon = data.canonical
+ const color = data.annotations.preferred ? "w3-text-flat-peter-river" : "";
+ const starIcon = data.annotations.canonical
? ``
: ``;
@@ -607,9 +611,9 @@ Comments ()
${starIcon}
-
${formatNA(data.HGVSg, "NA")}
-
${formatNA(data.HGVSc, "NA")}
-
${formatNA(data.HGVSp, "NA")}
+
${formatNA(data.annotations.HGVSg, "NA")}
+
${formatNA(data.annotations.HGVSc, "NA")}
+
${formatNA(data.annotations.HGVSp, "NA")}
${mobidetails}${genebe}${franklin}
@@ -618,9 +622,9 @@
Comments ()
`;
},
sort: (data) => {
- if (!data || !data.HGVSg) return -1;
+ if (!data.annotations || !data.annotations.HGVSg) return -1;
- const matches = data.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
+ const matches = data.annotations.HGVSg.match(/(chr|cen|pter|qter|sup)?([0-9XYMt]+):[gmno]\.([0-9]+)(_[0-9]+)?([ACGT]+>)?(dup|ins|del|inv|[ACGT]+)?/);
if (!matches) return -1;
const zero = "000000000";
@@ -896,10 +900,6 @@ Comments ()
const clinvar = data.clinvar || {};
const phenotypes = data.phenotypes || {};
const star = (clinvar.CLNREVSTAT == null) ? 0 : clinvar_stars[clinvar.CLNREVSTAT];
- if(clinvar.CLNREVSTAT == null){
- console.log(`${clinvar_stars[clinvar.CLNREVSTAT]} - ${clinvar.CLNREVSTAT}`)
- }
-
let stat = '';
if (clinvar.CLNREVSTAT) {
stat = ` (${star}/4)`;
@@ -951,7 +951,6 @@ Comments ()
color = "peter-river";
colorHover = "belize-hole";
if (/pathogenic|establish/i.test(clinvar.CLNSIGCONF)) {
- console.log(clinvar.CLNREVSTAT)
color = "carrot";
colorHover = "pumpkin";
}
@@ -1474,25 +1473,28 @@ Comments ()
}),
createColumn({
id: "export-filter-clinvar_revstat",
- data: "clinvar.CLNSIG",
+ data: null,
searchBuilderTitle:"ClinVar",
visible: false,
type: "clinvar",
renderConfig: {
default: (data) => {
- const clinvar = data || {};
+ const clinvar = data.clinvar || {};
let value = "2 - NA";
- if (clinvar) {
- if (/benign/i.test(clinvar)) value = "0 - Benign/Likely Benign";
- else if (/uncertain/i.test(clinvar)) value = "3 - Uncertain significance";
- else if (/pathogenic|establish/i.test(clinvar)) value = "5 - Pathogenic/Likely Pathogenic";
- else if (/conflicting/i.test(clinvar)) {
- value = "1 - Conflicting (without Pathogenic)";
- if (/pathogenic|establish/i.test(clinvar)) {
- value = "4 - Conflicting (with Pathogenic)";
+ if (clinvar.CLNSIG) {
+ if (/benign/i.test(clinvar.CLNSIG)) {
+ value = "0 - Benign/Likely Benign"
+ } else if (/uncertain/i.test(clinvar.CLNSIG)) {
+ value = "3 - Uncertain significance"
+ } else if (/conflicting/i.test(clinvar.CLNSIG)) {
+ value = "1 - Conflicting (without Pathogenic)"
+ if (/pathogenic|establish/i.test(clinvar.CLNSIGCONF)) {
+ value = "4 - Conflicting (with Pathogenic)"
}
- }
+ } else if (/pathogenic|establish/i.test(clinvar.CLNSIG)) {
+ value = "5 - Pathogenic/Likely Pathogenic"
+ }
}
return value;
},
@@ -1539,16 +1541,16 @@ Comments ()
}),
createColumn({
id: "export-filter-MES",
- data: "annotations",
+ data: null,
searchBuilderTitle:"Prediction - MaxEntScan",
visible: false,
renderConfig: {
default: (data, type) => {
- const alt = parseFloat(data.MaxEntScan_alt || 0).toFixed(2);
- const ref = parseFloat(data.MaxEntScan_ref || 0).toFixed(2);
+ const alt = parseFloat(data.annotations.MaxEntScan_alt || 0).toFixed(2);
+ const ref = parseFloat(data.annotations.MaxEntScan_ref || 0).toFixed(2);
const mes_var = (((alt - ref) / Math.abs(ref)) * 100).toFixed(2);
d = isNaN(parseFloat(mes_var)) ? null: parseFloat(mes_var).toFixed(2);
- return type === 'export' && d=== null? '' : data;
+ return type === 'export' && d=== null? '' : Math.abs(d);
},
}
}),
@@ -1560,7 +1562,7 @@ Comments ()
renderConfig: {
default: (data, type) => {
d = isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
- return type === 'export' && d=== null? '' : data;
+ return type === 'export' && d=== null? '' : d;
},
}
}),
@@ -1572,8 +1574,7 @@ Comments ()
renderConfig: {
default: (data, type) => {
d = isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
- return type === 'export' && d=== null? '' : data;
- return isNaN(parseFloat(data)) ? null: parseFloat(data).toFixed(2);
+ return type === 'export' && d=== null? '' : d;
},
}
}),
@@ -1658,7 +1659,7 @@ Comments ()
return `[${family.filter}] ${af} (${family.allelic_depth}/${family.depth})`;
},
}
- })
+ }),
{% endfor %}
];